Sat Oct 15 15:07:00 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 15 2011 at 15:07:00 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3130 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: SEP 234 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6613659 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -10.28800 37.41800 ymin,ymax (A): -27.31900 21.41500 zmin,zma (A): -8.315000 45.51300 x,y,z range (A): 47.70600 48.73400 53.82800 scale (grids/A): 0.6613659 object centre (A): 13.56500 -2.952001 18.59900 number of atom coordinates read : 3130 total number of charged atoms : 2719 net assigned charge : -2.298981 assigned positive charge : 433.8435 centred at (gu) : 89.49742 90.94917 91.32207 assigned negative charge : -436.1432 centred at (gu) : 89.24073 90.87730 91.23019 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8520 nv = 96 ne = 84 npr = 58655 no. pairs analyzed = 58655 no. exposed pairs = 3456 no. arc points = 23827 no. surface atoms = 1170 nbur = 1960 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 523 mr = 4986 m= 4 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3966 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2289 ## 217 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9956 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0825969E-08 1.9747992E-08 midg,1,midg; midg,igrid,midg -1.8666316E-08 1.2665158E-08 1,midg,midg; igrid,midg,midg -7.4176668E-08 4.6077425E-08 gauss-seidel spectral radius is 0.9881716 estimated iterations to convergence 75 setup time was (sec) 0.4200000 now iterating at: 15:07:00 rms-change max change #iterations 0.1831824 22.56802 at 10iterations 2.0022465E-02 2.563332 at 20iterations 2.2210781E-03 0.3714218 at 30iterations 2.8494257E-04 3.5289764E-02 at 40iterations 5.8071553E-05 6.4926147E-03 at 50iterations finished qdiffx linear iterations at : 15:07:03 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 5.8071553E-05 6.4926147E-03 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 15:07:04 3.565u 0.208s 0:04.04 93.0% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 15 2011 at 15:07:04 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3130 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: SEP 234 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.984097 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -10.28800 37.41800 ymin,ymax (A): -27.31900 21.41500 zmin,zma (A): -8.315000 45.51300 x,y,z range (A): 47.70600 48.73400 53.82800 scale (grids/A): 1.984097 object centre (A): 13.56500 -2.952001 18.59900 number of atom coordinates read : 3130 total number of charged atoms : 2719 net assigned charge : -2.298981 assigned positive charge : 433.8435 centred at (gu) : 88.49174 92.84718 93.96542 assigned negative charge : -436.1432 centred at (gu) : 87.72188 92.63153 93.69022 start vw surface at 0.1000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 91082 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23827 grid for indexing accessible points = 1.400000 m= 36304 mr = 65416 m= 6450 mr = 27952 m= 456 mr = 4229 m= 7 mr = 162 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 36540 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 128 iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 21463 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6613659 object centre at (A) : 13.56500 -2.952001 18.59900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0854521E-02 4.6869987E-03 midg,1,midg; midg,igrid,midg -1.3471312E-02 7.4783387E-04 1,midg,midg; igrid,midg,midg -2.9573929E-02 5.9781753E-02 gauss-seidel spectral radius is 0.9987620 estimated iterations to convergence 225 setup time was (sec) 0.7000000 now iterating at: 15:07:05 rms-change max change #iterations 4.950907 203.2366 at 10iterations 2.420464 80.08203 at 20iterations 1.174882 34.86916 at 30iterations 0.5719374 16.60841 at 40iterations 0.2785034 8.642553 at 50iterations 0.1354010 3.970848 at 60iterations 6.6015102E-02 1.685825 at 70iterations 3.2090642E-02 0.9193039 at 80iterations 1.5624638E-02 0.4792118 at 90iterations 7.5911763E-03 0.2305107 at 100iterations 3.6976936E-03 0.1011047 at 110iterations 1.8119033E-03 5.6212902E-02 at 120iterations finished qdiffx linear iterations at : 15:07:12 total time elapsed so far: 8.240000 # loops : 120 mean,max change (kT/e) : 1.8119033E-03 5.6212902E-02 energy calculations done at 8.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.370000 DelPhi exited at 15:07:13 8.368u 0.227s 0:08.93 96.0% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 15 2011 at 15:07:13 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3130 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: SEP 234 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.976146 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -10.28800 37.41800 ymin,ymax (A): -27.31900 21.41500 zmin,zma (A): -8.315000 45.51300 x,y,z range (A): 47.70600 48.73400 53.82800 scale (grids/A): 2.976146 object centre (A): 13.56500 -2.952001 18.59900 number of atom coordinates read : 3130 total number of charged atoms : 2719 net assigned charge : -2.298981 assigned positive charge : 433.8435 centred at (gu) : 87.73740 94.27058 95.94804 assigned negative charge : -436.1432 centred at (gu) : 86.58266 93.94723 95.53537 start vw surface at 0.1100000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 210369 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23827 grid for indexing accessible points = 1.400000 m= 114215 mr = 157666 m= 45455 mr = 95773 m= 12070 mr = 37616 m= 1926 mr = 9274 m= 137 mr = 1302 m= 4 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.220000 number of dielectric boundary points 82493 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 21752 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.984097 object centre at (A) : 13.56500 -2.952001 18.59900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2667527 0.3156465 midg,1,midg; midg,igrid,midg -0.1496313 3.6538683E-02 1,midg,midg; igrid,midg,midg -0.1864354 0.5348864 gauss-seidel spectral radius is 0.9992894 estimated iterations to convergence 296 setup time was (sec) 1.480000 now iterating at: 15:07:15 rms-change max change #iterations 11.25178 404.9286 at 10iterations 6.643054 135.0221 at 20iterations 3.898493 86.16747 at 30iterations 2.288458 43.74118 at 40iterations 1.339369 25.86936 at 50iterations 0.7850055 14.07340 at 60iterations 0.4594015 7.595185 at 70iterations 0.2676868 4.356773 at 80iterations 0.1566244 2.799059 at 90iterations 9.1209434E-02 1.602942 at 100iterations 5.3296741E-02 0.9507942 at 110iterations 3.1062912E-02 0.5429907 at 120iterations 1.8124700E-02 0.3064041 at 130iterations 1.0602204E-02 0.1676540 at 140iterations 6.2101595E-03 0.1042023 at 150iterations 3.6456727E-03 5.6823730E-02 at 160iterations 2.1631874E-03 3.8021088E-02 at 170iterations 1.2938166E-03 2.1826267E-02 at 180iterations finished qdiffx linear iterations at : 15:07:27 total time elapsed so far: 13.56000 # loops : 180 mean,max change (kT/e) : 1.2938166E-03 2.1826267E-02 energy calculations done at 13.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.69000 DelPhi exited at 15:07:27 13.687u 0.225s 0:14.17 98.0% 0+0k 0+0io 0pf+0w